Analysis of Codon Usage Bias and Phylogenesis in the Chloroplast Genome of Ancient Tea Tree Camellia taliensis in Forest-tea Garden

TONG Yan; HUANG Hui; WANG Yuhua

doi:10.13305/j.cnki.jts.2023.03.010

2023 , Vol. 43 >Issue 3: 297 - 309

DOI: https://doi.org/10.13305/j.cnki.jts.2023.03.010

Research Paper

Analysis of Codon Usage Bias and Phylogenesis in the Chloroplast Genome of Ancient Tea Tree Camellia taliensis in Forest-tea Garden

TONG Yan ,
HUANG Hui ,
WANG Yuhua

Expand

1. Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China;
2. Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, College of Biological and Food Engineering, Huaihua University, Huaihua 418000, China

Received date: 2023-02-13

Revised date: 2023-04-14

Online published: 2023-06-29

Fold

Abstract

Camellia taliensis is one of the important tea plants which is often grown in forest-tea gardens, which participated in the origin and domestication of C. sinensis var. assamica. To determine the codon usage bias pattern and its main influencing factors in the chloroplast genome of C. taliensis, neutral plotting, ENC-plot, PR2-plot analyses were performed and the optimal codons were found. The results show that the GC content of 54 CDS sequences was 37.68%, while GC₁ and GC₂ content were 46.44% and 39.77%, higher than GC₃(27.67%), indicating that the third base of the codon preferred to end in A/U. The effective codon number (ENC) ranged from 35.64 to 56.67 , with an average value of 46.1, demonstrating weak codon usage bias in chloroplast genome of C. taliensis. Neutral plotting, ENC-plot, PR2-plot analyses show that the main factor affecting the codon usage bias of the C. taliensis chloroplast genome was natural selection. In total, 11 optimal codons were identified in the chloroplast genome of C. taliensis. Although phylogenetic trees constructed by matK gene and CDS sequence display different topological structures, all trees show that C. taliensis and C. gymnogyna are clustered into one branch and are closely related to cultivated tea plant. This study provided the basis for analyses of genetic evolution, phylogeny and improved agronomic traits of C. taliensis.

Key words： Camellia taliensis; chloroplast genome; codon usage bias; forest-tea garden; phylogenetic analysis

Cite this article

TONG Yan , HUANG Hui , WANG Yuhua . Analysis of Codon Usage Bias and Phylogenesis in the Chloroplast Genome of Ancient Tea Tree Camellia taliensis in Forest-tea Garden[J]. Journal of Tea Science, 2023 , 43(3) : 297 -309 . DOI: 10.13305/j.cnki.jts.2023.03.010

References

[1] 虞富莲. 中国古茶树[M]. 昆明: 云南科技出版社, 2016.
Yu F L.Ancient tea plants in China[M]. Kunming: Yunnan Science and Technology Press, 2016.
[2] 蒋会兵, 唐一春, 陈林波, 等. 云南省古茶树资源调查与分析[J]. 植物遗传资源学报, 2020, 21(2): 296-307.
Jiang H B, Tang Y C, Chen L B, et al.Survey and analysis of ancient tea plant resources in Yunnan Province, China[J]. Journal of Plant Genetic Resources, 2020, 21(2): 296-307.
[3] 裴盛基, 苟祎, 耿彦飞, 等. 民族植物学视角下的森林茶园[J]. 中国茶叶, 2022, 44(12): 66-72.
Pei S J, Gou Y, Geng Y F, et al.Forest-tea garden from the perspective of ethnobotany[J]. China Tea, 2022, 44(12): 66-72.
[4] 刘德和, 殷丽琼, 宋维希, 等. 云南古茶园栽培管理技术研究[J]. 湖南农业科学, 2013(11): 12-14.
Liu D H, Yin L Q, Song W X, et al.Cultivation and management techniques for ancient tea plantation in Yunnan Province[J]. Hunan Agricultural Sciences, 2013(11): 12-14.
[5] 蒋会兵, 汪云刚, 唐一春, 等. 野生茶树大理茶种质资源现状调查[J]. 西南农业学报, 2009, 22(4): 1153-1157.
Jiang H B, Wang Y G, Tang Y C.Investigation of wild tea plant (Camellia taliensis), germplasm resource from Yunnan, China[J]. Southwest China Journal of Agricultural Sciences, 2009, 22(4): 1153-1157.
[6] 李金秋, 和明珠, 万人源, 等. 大理茶的研究进展[J]. 安徽农业科学, 2022, 50(8): 12-17.
Li J Q, He M Z, Wan R Y, et al.An overview of Camellia taliensis[J]. Journal of Anhui Agricultural Sciences, 2022, 50(8): 12-17.
[7] 刘阳, 杨世雄, 高立志. 云南古茶园栽培大叶茶和大理茶群体的叶绿体RPL32-TRNL核苷酸变异和遗传分化[J]. 云南植物研究, 2010, 32(5): 427-434.
Liu Y, Yang S X, Gao L Z.Comparative Study on the Chloroplast RPL32-TRNL nucleotide variation within and genetic differentiation among ancient tea plantations of Camellia sinensis var. assamica and C. taliensis (Theaceae) from Yunnan, China[J]. Plant Diversity, 2010, 32(5): 427-434.
[8] 李苗苗, Meegahakumbura M Kasun, 严丽君, 等. 核基因组微卫星标记揭示大理茶参与了普洱茶的驯化过程[J]. 植物分类与资源学报, 2015, 37(1): 29-37.
Li M M, Meegahakumbura M K, Yan L J, et al.Genetic involvement of Camellia taliensis in the domestication of C. sinensis var. assamica (Assimica tea) revealed by nuclear microsatellite markers[J]. Plant Diversity and Resources, 2015, 37(1): 29-37.
[9] 杨崇仁, 张颖君, 高大方, 等. 大理茶种质资源的评价与栽培大叶茶的起源[J]. 茶叶科学技术, 2008(3): 1-4.
Yang C R, Zhang Y J, Gao D F, et al.Evaluation of Camellia taliensis germplasm resources and origin of Camellia sinensis var. assamica[J]. Tea Science and Technology, 2008(3): 1-4.
[10] 唐一春, 杨盛美, 季鹏章, 等. 云南野生茶树资源的多样性、利用价值及其保护研究[J]. 西南农业学报, 2009, 22(2): 518-521.
Tang Y C, Yang S M, Ji P Z, et al.Study on the diversity, utilization and protection of wild tea germplasm in Yunnan[J]. Southwest China Journal of Agricultural Sciences, 2009, 22(2): 518-521.
[11] 陈佩. 茶园遮光效应及其对茶树光合作用和茶叶品质成分的影响[D]. 长沙: 湖南农业大学, 2010.
Chen P.Shading effects and influences on photosynthesis and quality component of tea in tea plantation[D]. Changsha: Hunan Agricultural University, 2010.
[12] 宛晓春, 夏涛. 茶树次生代谢[M]. 北京: 科学出版社, 2015.
Wan X C, Xia T.Secondary metabolism of tea plant[M]. Beijing: Science Press, 2015.
[13] 樊守金, 郭秀秀. 植物叶绿体基因组研究及应用进展[J]. 山东师范大学学报(自然科学版), 2022, 37(1): 22-31.
Fan S J, Guo X X.Advances in research and application of plant chloroplast genome[J]. Journal of Shandong Normal University (Natural Science), 2022, 37(1): 22-31.
[14] Hilu K W, Liang H P.The matK gene: sequence variation and application in plant systematics[J]. American Journal of Botany, 1997, 84(6): 830-839.
[15] Vogel J, Borner T, Hess W R.Comparative analysis of splicing of the complete set of chloroplast group Ⅱ introns in three higher plant mutants[J]. Nucleic Acids Research,1999, 27(19): 3866-3874.
[16] 聂传朋, 陈欣, 马欣耀, 等. 茶树DNA条形码引物的筛选[J/OL]. 分子植物育种, 2021: 1-11[2023-02-13]. http://kns.cnki.net/kcms/detail/46.1068.s.20210916.1316.026.html.
Nie C P, Chen X, Ma X Y, et al.Screening of primers for DNA barcoding of tea plant[J]. Molecular Plant Breeding, 2021: 1-11[2023-02-13]. Screening of primers for DNA barcoding of tea plant[J]. Molecular Plant Breeding, 2021: 1-11[2023-02-13]. http://kns.cnki.net/kcms/detail/46.1068.s.20210916.1316.026.html.
[17] Hershberg R, Petrov D A.Selection on codon bias[J]. Annual Review of Genetics, 2008, 42: 287-299.
[18] Adi Y, Sophia K, Ruth H.The codon usage of lowly expressed genes is subject to natural selection[J]. Genome Biology and Evolution, 2018, 10(5): 1237-1246.
[19] 吴宪明, 吴松锋, 任大明, 等. 密码子偏性的分析方法及相关研究进展[J]. 遗传, 2007, 29(4): 420-426.
Wu X M, Wu S F, Ren D M, et al.The analysis method and progress in the study of codon bias[J]. Hereditas (Beijing), 2007, 29(4): 420-426.
[20] Yang J B, Yang S X, Li H T, et al. Comparative chloroplast genomes of Camellia species[J]. Plos One, 2013, 23, 8(8): e73053. doi: 10.1371/journal.pone.0073053.
[21] Liu X.A more accurate relationship between ‘effective number of codons’ and GC3s under assumptions of no selection[J]. Computational biology and chemistry, 2013, 42: 35-39.
[22] Wright F.The ‘effective number of codons’ used in a gene[J]. Gene, 1990, 87(1): 23-29.
[23] 杨国锋, 苏昆龙, 赵怡然, 等. 蒺藜苜蓿叶绿体密码子偏好性分析[J]. 草业学报, 2015, 24(12): 171-179.
Yang G F, Su K L, Zhao Y R, et al.Analysis of codon usage in the chloroplast genome of Medicago truncatula[J]. Acta Prataculturae Sinica, 2015, 24(12): 171-179.
[24] Sueoka N.Near homogeneity of PR2-bias fingerprints in the human genome and their implications in phylogenetic analyses[J]. Journal of Molecular Evolution, 2001, 53(4/5): 469-476.
[25] Duret L, Mouchiroud D.Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis[J]. PNAS, 1999, 96(8): 4482-4487.
[26] 张宏达. 山茶属植物的系统研究[M]. 广州: 中山大学出版社, 1981.
Chang H D.A taxonomy of the genus Camellia[M]. Guangzhou: Sun Yat-sen University Press, 1981.
[27] 张宏达. 茶叶植物资源的订正[J]. 中山大学学报(自然科学版), 1984, 23(1): 1-12.
Chang H T.A revision on the tea resource plants[J]. Acta Scientiarum Naturalium Uinversitatis Sunyatseni, 1984, 23(1): 1-12.
[28] 闵天禄. 山茶属茶组植物的订正[J]. 云南植物研究, 1992, 14(2): 115-132.
Ming T L.A revision of camellia Sect. Thea[J]. Acta Botanica Yunnanica, 1992, 14(2): 115-132.
[29] 闵天禄. 世界山茶属的研究[M]. 昆明: 云南科技出版社, 2000.
Ming T L.Monograph of the genus Camellia[M]. Kunming: Yunnan Science and Technology Press, 2000.
[30] 陈亮, 虞富莲, 童启庆. 关于茶组植物分类与演化的讨论[J]. 茶叶科学, 2000, 20(2): 89-94.
Chen L, Yu F L, Tong Q Q.Discussions on phylogenetic classification and evolution of Sect. Thea[J]. Journal of Tea Science, 2000, 20(2): 89-94.
[31] 杜琪珍, 李名君, 刘维华, 等. 茶组植物的化学分类及数值分类[J]. 茶叶科学, 1990, 10(2): 1-12.
Du Q Z, Li M J, Liu W H, et al.Chemical and numerical taxonimies of plants Thea Section plants[J]. Journal of Tea Science, 1990, 10(2): 1-12.
[32] Parks C R.Cross-compatibility studies in the genus Camellia[J]. International Camellia Journal, 1990, 22: 37-54.
[33] Huang H, Shi C, Liu Y, et al.Thirteen Camellia chloroplast genome sequences determined by high-throughput sequencing: genome structure and phylogenetic relationships[J]. BMC evolutionary biology, 2014, 14(1): 151. doi: 10.1186/1471-2148-14-151.
[34] Vijayan K, Zhang W J, Tsou C H.Molecular taxonomy of Camellia (Theaceae) inferred from nrITS sequences[J]. American Journal of Botany, 2009, 96(7): 1348-1360.
[35] Wachira F N, Tanaka J, Takeda Y.Genetic variation and differentiation in tea (Camellia sinensis) germplasm revealed by RAPD and AFLP variation[J]. The Journal of Horticultural Science and Biotechnology, 2001, 76(5): 557-563.
[36] Wang L Y, Liu B Y, Jiang Y H, et al.Phylogenetic analysis of inter species in section Thea through SSR markers[J]. Journal of the Science, 2009, 29(5): 341-346.
[37] 陈亮, 山口聪, 王平盛, 等. 利用RAPD进行茶组植物遗传多样性和分子系统学分析[J]. 茶叶科学, 2002, 22(1): 19-24.
Chen L, Satoshi Y, Wang P S, et al.Genetic polymorphism and molecular phylogeny analysis of section Thea based on RAPD markers[J]. Journal of Tea Science, 2002, 22(1): 19-24.
[38] 季鹏章, 汪云刚, 张俊, 等. 茶组植物亲缘关系的ISSR分析[J]. 西南农业学报, 2009, 22(3): 584-588.
Ji P Z, Wang Y G, Zhang J, et al.Genetic relationships between Sect. Thea from Yunnan province revealed by inter-simple sequence repeat polymerase China reaction[J]. Southwest China J Agricultural Sciences, 2009, 22(3): 584-588.
[39] 田敏, 李纪元, 倪穗, 等. 基于ITS序列的红山茶组植物系统发育关系的研究[J]. 园艺学报, 2008, 35(11): 1685-1688.
Tian M, Li J Y, Ni S, et al.Phylogenetic study on section Camellia based on ITS sequences data[J]. Acta Horticulturae Sinica, 2008, 35(11): 1685-1688.
[40] Wu Q, Tong W, Zhao H J, et al.Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants[J]. The Plant Journal, 2022, 11(2): 406-421.
[41] Chen S Y, Li K, Cao W Q, et al.Codon-resolution analysis reveals a direct and context-dependent impact of individual synonymous mutations on mRNA level[J]. Molecular Biology and Evolution, 2017, 34(11): 2944-2958.
[42] Carlini D B, Ying C, Stephan W.The relationship between third-codon position nucleotide content, codon bias, mRNA secondary structure and gene expression in the drosophilid alcohol dehydrogenase genes Adh and Adhr[J]. Genetics, 2001, 159(2): 623-633.
[43] Stenstrom C M, Jin H, Major L L, et al.Codon bias at the 3'-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli[J]. Gene, 2001, 263(1/2): 273-284.
[44] 石秀凡, 黄京飞, 柳树群, 等. 人类基因同义密码子偏好的特征以及与基因GC含量的关系[J]. 生物化学与生物物理进展, 2002, 29(3): 411-414.
Shi X F, Huang J F, Liu S Q, et al.The features of synonymous codon bias and GC-content relationship in human genes[J]. Progress in Biochemistry and Biophysics, 2002, 29(3): 411-414.
[45] Moriyama E N, Powell J R.Codon usage bias and tRNA abundance in Drosophila[J]. Journal of Molecular Evolution, 1997, 45(5): 514-523.
[46] 王鹏良, 杨利平, 吴红英, 等. 普通油茶叶绿体基因组密码子偏好性分析[J]. 广西植物, 2018, 38(2): 135-144.
Wang P L, Yang L P, Wu H Y, et al.Condon preference of chloroplast genome in Camellia oleifera[J]. Guihaia, 2018, 38(2): 135-144.
[47] 滕腾, 赵懿琛, 赵德刚. 鸟王茶基因密码子偏好性分析[J]. 基因组学与应用生物学, 2021, 40(2): 795-801.
Teng T, Zhao Y C, Zhao D G.Analysis of genetic codon preference of Camellia sinensis var. niaowangensis[J]. Genomics and Applied Biology, 2021, 40(2): 795-801.
[48] 郝丙青, 夏莹莹, 叶航, 等. 香花油茶叶绿体基因组密码子偏好性分析[J]. 中南林业科技大学学报, 2022, 42(9): 178-186.
Hao B Q, Xia Y Y, Ye H, et al.Analysis on codon usage bias of the chloroplast genome of Camellia osmantha[J]. Journal of Central South University of Forestry & Technology, 2022, 42(9): 178-186.
[49] Campbell W H, Gowri G.Codon usage in higher plants, green algae, and cyanobacteria[J]. Plant Physiology, 1990, 92(1): 1-11.
[50] Sealy J R.A revision of the genus Camellia[M]. London: The Royal Horticultural Society, 1958.
[51] Li L, Hu Y F, He M, et al.Comparative chloroplast genomes: insights into the evolution of the chloroplast genome of Camellia sinensis and the phylogeny of Camellia[J]. BMC Genomics, 2021, 22(1): 138. doi: 10.1186/s12864-021-07427-2.
[52] 赵东伟, 杨世雄. 山茶科大苞茶的再发现及形态特征修订[J]. 热带亚热带植物学报, 2012, 20(4): 399-402.
Zhao D W, Yang S X.Rediscovery of Camellia grandibracteata (Theaceae) with emendate description[J]. Journal of Tropical and Subtropical Botany, 2012, 20(4): 399-402.

Options

Outlines

模态框（Modal）标题

Abstract

Cite this article

References